SMTL ID : 3ras.1

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with a lipophilic phosphonate inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: G.28, S.29, T.30, G.31, S.32, I.33, A.55, G.56, G.57, A.58, H.59, A.78, A.112, L.113, V.114, L.117, A.135, N.136, K.137, E.138, D.160, M.214, G.215, P.216, N.218, M.276 Ligands: FM5.2, DCV.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.33 Hydrogen bonds: A:G.28, A:T.30, A:T.30, A:T.30, A:S.32, A:S.32, A:S.32, A:I.33, A:G.56, A:G.57, A:A.58, A:H.59, A:L.113, A:V.114, A:N.136, A:K.137, A:G.215, A:N.218 Water bridges: A:G.34 Salt bridges: A:H.59 NDP.5: 21 residues within 4Å: Chain B: G.28, S.29, T.30, G.31, S.32, I.33, A.55, G.56, G.57, A.58, H.59, A.78, A.112, L.113, V.114, L.117, A.135, N.136, K.137, D.160, M.276 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.28, B:T.30, B:T.30, B:T.30, B:G.31, B:S.32, B:S.32, B:S.32, B:I.33, B:G.56, B:G.57, B:A.58, B:H.59, B:L.113, B:N.136, B:K.137 Water bridges: B:G.34, B:E.138 Salt bridges: B:H.59

2 x FM5: 3-(N-HYDROXYACETAMIDO)-1-(3,4-DICHLOROPHENYL)PROPYLPHOSPHONIC ACID(Non-covalent)

FM5.2: 20 residues within 4Å: Chain A: D.160, S.161, E.162, A.185, S.186, H.209, W.212, M.214, N.218, S.222, N.227, K.228, E.231, S.254, H.257, P.274, M.276 Ligands: NDP.1, DCV.3, MN.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.137, A:S.161, A:S.186, A:N.227, A:K.228, A:K.228, A:K.228 FM5.6: 6 residues within 4Å: Chain B: T.30, H.59, T.62, R.65, W.212 Ligands: DCV.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.212 pi-Stacking: B:H.59 Halogen bonds: B:T.30

2 x DCV: [(1R)-3-[acetyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid(Non-covalent)

DCV.3: 20 residues within 4Å: Chain A: K.137, D.160, S.161, E.162, A.185, S.186, H.209, W.212, M.214, N.218, S.222, N.227, K.228, E.231, S.254, P.274, M.276 Ligands: NDP.1, FM5.2, MN.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.137, A:S.161, A:E.162, A:S.186, A:G.187, A:N.227, A:K.228, A:K.228 DCV.7: 5 residues within 4Å: Chain B: T.30, H.59, T.62, W.212 Ligands: FM5.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.212 Water bridges: B:D.61 pi-Stacking: B:H.59

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 7 residues within 4Å: Chain A: K.137, D.160, S.161, E.162, E.231 Ligands: FM5.2, DCV.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.160, A:E.162, A:E.231 MN.8: 3 residues within 4Å: Chain B: D.160, E.162, E.231 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.160, B:D.160, B:E.162, B:E.231, H2O.5

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain B: A.185, S.186, S.222, N.227, K.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.186, B:N.227 Water bridges: B:G.187, B:S.222 Salt bridges: B:K.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, L. et al., Inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase by lipophilic phosphonates: SAR, QSAR, and crystallographic studies. J.Med.Chem. (2011)

Release Date

2011-05-25

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase

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